In Silico and Experimental Data Claiming Safety Aspects and Beneficial Attributes of the Bacteriocinogenic Strain Enterococcus faecalis B3A-B3B Alaa Al Seraih 1 & Yanath Belguesmia 1 & Benoit Cudennec 1 & John Baah 2 & Djamel Drider 1 # Springer Science+Business Media, LLC, part of Springer Nature 2017 Abstract This study aimed at comparing the genome of Enterococcus faecalis B3A-B3B, a bacteriocinogenic strain recently isolated from a healthy Iraqi infant to those of Enterococci of clinical and beneficial grades. The putative genes gelE, cpd, efaAfm, ccf, agg, and cob coding for virulence factors were detected in B3A-B3B strain, which meanwhile resulted to be non-cytotoxic, non-hemo- lytic, devoid of inflammatory effects, and sensitive to most of the antibiotics tested except for clindamycin and trimethoprim, which resistance is usually ascribed to intrinsic nature. B3A-B3B strain was remarkable for its hydrophobicity, auto-aggregation, adhesion to human Caco-2 cells, and survival in simulated gastrointestinal conditions, and cholesterol assimilation fulfilling therefore key beneficial attributes. Keywords Lactic acid bacteria . Enterococcus faecalis . Beneficial traits . Bacteriocin . In silico analysis Introduction Majority of lactic acid bacteria (LAB) are generally recog- nized as safe (GRAS) microorganisms, which are isolated from different sources including plants, fermented foods, humans, and animals [1]. LAB constitute a substantial part of the human or animal microbiota, they are abundantly found in the gastrointestinal (GIT), and the genitourinary tracts, along with other bacterial species and other microbes [2, 3]. Enterococci are part of LAB group with capabilities to grow under harsh conditions including highly elevated bile salts concentrations (up to 40%), temperatures ranging from 10 to 45 °C, NaCl concentration up to 6.5%, and pH 9.6 [4, 5]. Enterococci can be found in many ecological niches including traditional fermented food and dairy products, water, soil, and plants [6]. These microbes are adapted members of the GIT of humans, mammals, reptiles, birds, and insects [6–8]. Enterococci are studied for their role in life-threatening infections in humans, but also for their beneficial attributes for food products and probiotics. Arias and Murray [9] con- sidered these microbes as a major cause of healthcare- associated infections worldwide. Pericás et al. [10] associated Enterococci with the third cause of infective endocarditis (IE) worldwide. Vancomycin-resistant enterococci (VRE) known as opportunistic pathogens in the immunocompromised pop- ulations can easily grow and colonize the GIT of patients. Antibiotic treatment of VRE infections could lead to dysbiosis and persistence of VRE in the GIT [11]. E. faecalis and E. faecium are the most species clinically relevant because of their role in endocartidis, urinary tract infections, meningitis, and bacteremia [12, 13]. These examples taken from a myriad of cases reports delineate the worrisome side of this microbe. Enterococci were isolated from different fermented foods and used as starter cultures for artisanal food products [14, 15]. Their food application has to be limited for strains free of genes coding for virulence factors and antibiotic resistance [16]. These criteria are difficult to fulfill because Enterococci can easily and naturally acquire outside DNA as mobile ge- netic elements, which can include virulence and antibiotic resistance genes [14]. On the other hand, the role of Enterococci in the prevention of the intestinal overgrowth or colonization by bacterial path- ogens was evidenced [ 17 ]. Enterococci strains with established probiotic hallmarks include E. faecalis Symbioflor 1 [13], E. faecalis DSM 16440 [18], E. faecalis PC1.1 [19], and E. faecalis EC12 [20]. The use of enterococci * Yanath Belguesmia yanath.belguesmia@polytech-lille.fr 1 Université de Lille, INRA, ISA, Université d’Artois, Université du Littoral-Côte d’Opale, EA 7394 Institut Charles Viollette, 59000 Lille, France 2 Best Environmental Technologies Inc, 9610-39 Avenue NW, Edmonton, Alberta T6E 5T9, Canada Probiotics and Antimicrobial Proteins https://doi.org/10.1007/s12602-017-9357-8